Fine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1

FIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato

Fruit firmness is a target trait in tomato breeding because it facilitates transportation and storage. However, it is also a complex trait and uncovering the molecular genetic mechanisms controlling fruit firmness has proven challenging. Here, we report the map-based cloning and functional characterization of qFIRM SKIN 1 (qFIS1), a major quantitative trait locus that partially determines the difference in compression resistance between cultivated and wild tomato accessions. FIS1 encodes a GA2-oxidase, and its mutation leads to increased bioactive gibberellin content, enhanced cutin and wax biosynthesis, and increased fruit firmness and shelf life. Importantly, FIS1 has no unfavorable effect on fruit weight or taste, making it an ideal target for breeders. Our study demonstrates that FIS1 mediates gibberellin catabolism and regulates fruit firmness, and it offers a potential strategy for tomato breeders to produce firmer fruit.

Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L

QTL and candidate genes associated to fruit quality traits have been identified in a tomato genetic map derived from Solanum pimpinellifolium L., providing molecular tools for marker-assisted breeding. The study of genetic, physiological, and molecular pathways involved in fruit development and ripening has considered tomato as the model fleshy-fruited species par excellence. Fruit quality traits regarding organoleptic and nutritional properties are major goals for tomato breeding programs since they largely decide the acceptance of tomato in both fresh and processing markets. Here we report the genetic mapping of single-locus and epistatic quantitative trait loci (QTL) associated to the fruit size and content of sugars, acids, vitamins, and carotenoids from the characterization of a RIL population derived from the wild-relative Solanum pimpinellifolium TO-937. A genetic map composed of 353 molecular markers including 13 genes regulating fruit and developmental traits was generated, which spanned 1007 cM with an average distance between markers of 2.8 cM. Genetic analyses indicated that fruit quality traits analyzed in this work exhibited transgressive segregation and that additive and epistatic effects are the major genetic basis of fruit quality traits. Moreover, most mapped QTL showed environment interaction effects. FrW7.1 fruit size QTL co-localized with QTL involved in soluble solid, vitamin C, and glucose contents, dry weight/fresh weight, and most importantly with the Sucrose Phosphate Synthase gene, suggesting that polymorphisms in this gene could influence genetic variation in several fruit quality traits. In addition, 1-deoxy-D-xylulose 5-phosphate synthase and Tocopherol cyclase genes were identified as candidate genes underlying QTL variation in beta-carotene and vitamin C. Together, our results provide useful genetic and molecular information regarding fruit quality and new chances for tomato breeding by implementing marker-assisted selection.

Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites

When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ∼30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato.

Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology

Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipaënsis×A. duranensis)(4x) and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line×trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies.

Gene discovery in cereals through quantitative trait loci and expression analysis in water-use efficiency measured by carbon isotope discrimination

Drought continues to be a major constraint on cereal production in many areas, and the frequency of drought is likely to increase in most arid and semi-arid regions under future climate change scenarios. Considerable research and breeding efforts have been devoted to investigating crop responses to drought at various levels and producing drought-resistant genotypes. Plant physiology has provided new insights to yield improvement in drought-prone environments. Crop performance could be improved through increases in water use, water-use efficiency (WUE) and harvest index. Greater WUE can be achieved by coordination between photosynthesis and transpiration. Carbon isotope discrimination (Δ(13) C) has been demonstrated to be a simple but reliable measure of WUE, and negative correlation between them has been used to indirectly estimate WUE under selected environments. New tools, such as quantitative trait loci (QTL) mapping and gene expression profiling, are playing vital roles in dissecting drought resistance-related traits. The combination of gene expression and association mapping could help identify candidate genes underlying the QTL of interest and complement map-based cloning and marker-assisted selection. Eventually, improved cultivars can be produced through genetic engineering. Future efficient and effective breeding progress in cereals under targeted drought environments will come from the integrated knowledge of physiology and genomics.

Mode of inheritance of primary metabolic traits in tomato

To evaluate components of fruit metabolic composition, we have previously metabolically phenotyped tomato (Solanum lycopersicum) introgression lines containing segmental substitutions of wild species chromosome in the genetic background of a cultivated variety. Here, we studied the hereditability of the fruit metabolome by analyzing an additional year's harvest and evaluating the metabolite profiles of lines heterozygous for the introgression (ILHs), allowing the evaluation of putative quantitative trait locus (QTL) mode of inheritance. These studies revealed that most of the metabolic QTL (174 of 332) were dominantly inherited, with relatively high proportions of additively (61 of 332) or recessively (80 of 332) inherited QTL and a negligible number displaying the characteristics of overdominant inheritance. Comparison of the mode of inheritance of QTL revealed that several metabolite pairs displayed a similar mode of inheritance of QTL at the same chromosomal loci. Evaluation of the association between morphological and metabolic traits in the ILHs revealed that this correlation was far less prominent, due to a reduced variance in the harvest index within this population. These data are discussed in the context of genomics-assisted breeding for crop improvement, with particular focus on the exploitation of wide biodiversity.

Quantitative genetic analysis of flowering time in tomato

Artificial selection of cultivated tomato (Solanum lycopersicum L.) has resulted in the generation of early-flowering, day-length-insensitive cultivars, despite its close relationship to other Solanum species that need more time and specific photoperiods to flower. To investigate the genetic mechanisms controlling flowering time in tomato and related species, we performed a quantitative trait locus (QTL) analysis for flowering time in an F2 mapping population derived from S. lycopersicum and its late-flowering wild relative S. chmielewskii. Flowering time was scored as the number of days from sowing to the opening of the first flower (days to flowering), and as the number of leaves under the first inflorescence (leaf number). QTL analyses detected 2 QTLs affecting days to flowering, which explained 55.3% of the total phenotypic variance, and 6 QTLs for leaf number, accounting for 66.7% of the corresponding phenotypic variance. Four of the leaf number QTLs had not previously been detected for this trait in tomato. Colocation of some QTLs with flowering-time genes included in the genetic map suggests PHYB2, FALSIFLORA, and a tomato FLC-like sequence as candidate genes that might have been targets of selection during the domestication of tomato.

Analysis of the chromosome 2(2H) region of barley associated with the correlated traits Fusarium head blight resistance and heading date

Fusarium head blight (FHB) is a major disease of barley (Hordeum vulgare L.) that results in reduced grain yield and quality through the accumulation of the mycotoxin deoxynivalenol (DON). Coincident QTL for FHB severity, DON concentration, and heading date (HD) map to a region of chromosome 2(2H) designated Qrgz-2H-8. It is unclear whether disease resistance at this locus is due to a pleiotropic effect of late HD by delaying the host exposure to the pathogen or a tightly linked resistance gene. The objectives of this study were to develop a set of near isogenic lines (NILs) for the Qrgz-2H-8 region and to genetically dissect the QTL region containing the coincident traits. Two NIL populations were developed consisting of F(2)- and F(4)-derived recombinants from a cross between a BC(5) line carrying the donor parent (Chevron) alleles in the Qrgz-2H-8 region and the recurrent parent M69. Analysis of field and marker data from these NILs revealed that the Chevron alleles conditioning FHB resistance, late HD, and low DON concentration were successfully introgressed into the BC(5) parent line and were segregating among NILs. QTL analysis of the F(4)-derived population showed that the HD QTL is adjacent to the FHB QTL. Furthermore, a single NIL was identified that was similar to the resistant BC(5) parent for FHB severity and the early flowering parent M69 for HD. These results indicate that the relationship between FHB and HD at the Qrgz-2H-8 region is likely due to tight linkage rather than pleiotropy.

Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley

Hordeum vulgare subsp. spontaneum, the wild progenitor of barley, is a potential source of useful genetic variation for barley breeding programs. The objective of this study was to map quantitative trait loci (QTLs) in an advanced backcross population of barley. A total of 207 BC3 lines were developed using the 2-rowed German spring cultivar Hordeum vulgare subsp. vulgare 'Brenda' as a recurrent parent and the H. vulgare subsp. spontaneum accession HS584 as a donor parent. The lines were genotyped by 108 simple-sequence repeat (SSR) markers and evaluated in field tests for the measurement of grain yield and its components, such as ear length, spikelet number per spike, grain number per spike, spike number, and 1000-grain mass, as well as heading date and plant height. A total of 100 QTLs were detected. Ten QTLs with increasing effects were found for ear length, spikelet number, and grain number per spike. Three QTLs contributed by HS584 were found to significantly decrease days to heading across all years at 2 locations. In addition, 2 QTLs from HS584 on chromosomes 2H and 3H were associated with resistance to leaf rust. Based on genotypic data obtained from this population, 55 introgression lines carrying 1 or 2 donor segments were selected to develop a set of doubled-haploid lines, which will be used to reconfirm and investigate the effects of 100 QTLs for future genetic studies.

Natural genetic variation for improving crop quality

The narrow genetic basis of many crops combined with restrictions on the commercial use of genetically modified plants, has led to a surge of interest in exploring natural biodiversity as a source of novel alleles to improve the productivity, adaptation, quality and nutritional value of crops. Genetic methodologies have been applied to natural variation to improve quality aspects that are associated with the chemical composition of agricultural products. A future challenge in this emerging field is to integrate metabolic, phenotypic and genomic databases to allow a wider view of the plant metabolome and the application of this knowledge within genomics-assisted breeding.

Development of candidate introgression lines using an exotic barley accession ( Hordeum vulgare ssp. spontaneum) as donor

In the present paper, we report on the selection of two sets of candidate introgression lines (pre-ILs) in spring barley. Two BC2DH populations, S42 and T42, were generated by introgressing an accession of Hordeum vulgare ssp. spontaneum (ISR42-8, from Israel) into two different spring barley cultivars, Scarlett (S) and Thuringia (T). From these BC2DH populations two sets with 49 (S42) and 43 (T42) pre-ILs were selected, and their genomic architecture as revealed by SSR marker analysis was characterised. The selected pre-ILs cover at least 98.1% (S42) and 93.0% (T42) of the exotic genome in overlapping introgressions and contain on average 2 (S42) and 1.5 (T42) additional non-target introgressions. In order to illustrate a potential application and validation of these pre-ILs, the phenotypic effect of the exotic introgression at the locus of the major photoperiod response gene Ppd-H1 was analysed. Pre-ILs carrying the introgression at the Ppd-H1 locus flowered significantly earlier than the elite parents, and the introgression maintained its effect across the two genetic backgrounds and across four tested environments. The selected pre-ILs represent a first promising step towards the assessment and utilization of genetic variation present in exotic barley. They may promote the breeding progress, serve for the verification of QTL effects and provide a valuable resource for the unravelling of gene function, e.g. by expression profiling or map-based cloning.

Advanced backcross QTL analysis of a Lycopersicon esculentum x L. pennellii cross and identification of possible orthologs in the Solanaceae

In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC(2) plants were genotyped with 150 molecular markers and BC(2)F(1) plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs ( fsz2b.1, fw3.1/ fsz3.1 and fs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.